Identification of major sequence types among aminoglycoside resistant Staphylococcus aureus and Staphylococcus epidermidis strains isolated from clinical samples
Abstract
Background and Objectives: Aminoglycosides have been widely used for treating severe staphylococcal infections. Production aminoglycoside modifying enzymes (AMEs) is the main mechanism of resistance to this antibiotic. The aim of this study was to determine the prevalence of AME genes and molecular characterization of aminoglycoside-resistant Staphylococcus aureus and Staphylococcus epidermidis strains isolated from clinical specimens in Iran.
Materials and Methods: A total of 42 clinical isolates of Gram-positive cocci (20 S. aureus and 22 S. epidermidis) with resistance to gentamicin were tested for antimicrobial resistance and differentiated by multilocus sequence typing (MLST).
Results: All 42 isolates were resistant to methicillin, kanamycin,and most of them were also resistant to amikacin (98%), tobramycin (98%) and netilmycin (78.5%). Overall, aac(6’)-Ie-aph(2’’)-Ia was the dominant AME gene found in 100% of isolates, followed by aph(3')IIIa found in 90% of isolates. MLST classified S. aureus and S. epidermidis into 5 and 9 distinct sequence types (ST), respectively. The majority of the strains belonged to ST239 (50%) for S. aureus and ST2 (36%) for S. epidermidis.
Conclusion: The resistance to aminoglycosides was mainly due to the presence of the aac(6’)-Ie-aph(2’’)-Ia and aph(3')IIIa genes as well as the ST239 for S. aureus and ST2 for S. epidermidis have become the predominant clones in the selected university hospital of Tehran, Iran. Thus, it is critical that clinicians and healthcare workers are aware of the population of S. aureus and S. epidermidis present in order to make decisions for appropriate treatment and infection control practices.
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2. Liakopoulos A, Foka A, Vourli S, Zerva L, Tsiapara F, Protonotariou E, et al. Aminoglycoside-resistant staphylococci in Greece: prevalence and resistance mechanisms. Eur J Clin Microbiol Infect Dis 2011; 30: 701-705.
3. Ramirez MS, Nikolaidis N, Tolmasky ME. Rise and dissemination of aminoglycoside resistance: the 33paradigm. Front Microbiol 2013; 4: 121.
4. Garneau-Tsodikova S, Labby KJ. Mechanisms of resistance to aminoglycoside antibiotics: overview and perspectives. Medchemcomm 2016; 7: 11-27.
5. Sabat AJ, Budimir A, Nashev D, Sá-Leão R, van Dijl J, Laurent F, et al. Overview of molecular typing methods for outbreak detection and epidemiological surveillance. Euro Surveill 2013; 18: 20380.
6. Enright MC, Day NP, Davies CE, Peacock SJ, Spratt BG. Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus. J Clin Microbiol 2000; 38: 1008-1015.
7. Thomas JC, Robinson DA. Multilocus sequence typing of Staphylococcus epidermidis. Methods Mol Biol 2014; 1106:61-69.
8. Conceição T, Aires-de-Sousa M, Füzi M, Tóth A, Pászti J, Ungvári E, et al. Replacement of methicillin-resistant Staphylococcus aureus clones in Hungary over time: a 10-year surveillance study. Clin Microbiol Infect 2007; 13: 971-979.
9. Mahon CR, Lehman DC, Manuselis Jr G. Textbook of Diagnostic Microbiology. 6th edition.New York: Saunders; 2019. p: 307-319.
10. Hirotaki S, Sasaki T, Kuwahara-Arai K, Hiramatsu K. Rapid and accurate identification of human-associated staphylococci by use of multiplex PCR. J Clin Microbiol 2011; 49: 3627-3631.
11. Clinical and Laboratory Standards Institute (CLSI). Performance standards for antimicrobial susceptibility testing. 27th ed. CLSI supplement M100. Wayne, PA: Clinical and Laboratory Standards Institute; 2017.
12. Emaneini M, Taherikalani M, Eslampour MA, Sedaghat H, Aligholi M, Jabalameli F, et al. Phenotypic and genotypic evaluation of aminoglycoside resistance in clinical isolates of staphylococci in Tehran, Iran. Microb Drug Resist 2009; 15: 129-132.
13. Nascimento M, Sousa A, Ramirez M, Francisco AP, Carriço JA, Vaz C. PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods. Bioinformatics 2017; 33: 128-129.
14. Cheng H, Yuan W, Zeng F, Hu Q, Shang W, Tang D, et al. Molecular and phenotypic evidence for the spread of three major methicillin-resistant Staphylococcus aureus clones associated with two characteristic antimicrobial resistance profiles in China. J Antimicrob Chemother 2013;68:2453-2457.
15. Seyedi-Marghaki F, Kalantar-Neyestanaki D, Saffari F, Hosseini-Nave H, Moradi M. Distribution of aminoglycoside-modifying enzymes and molecular analysis of the coagulase gene in clinical isolates of methicillin-resistant and methicillin-susceptible Staphylococcus aureus. Microb Drug Resist 2019; 25: 47-53.
16. Yadegar A, Sattari M, Mozafari NA, Goudarzi GR. Prevalence of the genes encoding aminoglycoside-modifying enzymes and methicillin resistance among clinical isolates of Staphylococcus aureus in Tehran, Iran. Microb Drug Resist 2009; 15: 109-113.
17. Yuan W, Liu J, Zhan Y, Wang L, Jiang Y, Zhang Y, et al. Molecular typing revealed the emergence of pvl-positive sequence type 22 methicillin-susceptible Staphylococcus aureus in Urumqi, Northwestern China. Infect Drug Resist 2019;12:1719-1728.
18. Chen CJ, Huang YC. New epidemiology of Staphylococcus aureus infection in Asia. Clin Microbiol Infect 2014;20:605-623.
19. Lakhundi S, Zhang K. Methicillin-resistant Staphylococcus aureus: molecular characterization, evolution, and epidemiology. Clin Microbiol Rev 2018; 31(4):e00020-18.
20. Havaei SA, Vidovic S, Tahmineh N, Mohammad K, Mohsen K, Starnino S, et al. Epidemic methicillin-susceptible Staphylococcus aureus lineages are the main cause of infections at an Iranian university hospital. J Clin Microbiol 2011; 49: 3990-3993.
21. Goudarzi M, Bahramian M, Satarzadeh Tabrizi M, Udo EE, Figueiredo AM, Fazeli M, et al. Genetic diversity of methicillin resistant Staphylococcus aureus strains isolated from burn patients in Iran: ST239-SCCmec III/t037 emerges as the major clone. Microb Pathog 2017; 105: 1-7.
22. Goudarzi M, Goudarzi H, AM SF, Udo EE, Fazeli M, Asadzadeh M, et al. Molecular characterization of methicillin resistant Staphylococcus aureus strains isolated from intensive care units in Iran: ST22-SCCmec IV/t790 emerges as the major clone. PLoS One 2016; 11(5):e0155529.
23. Zhou YP, Wilder-Smith A, Hsu LY. The role of international travel in the spread of methicillin-resistant Staphylococcus aureus. J Travel Med 2014; 21: 272-281.
24. Boswihi SS, Udo EE, Al-Sweih N. Shifts in the clonal distribution of methicillin-resistant Staphylococcus aureus in Kuwait hospitals: 1992-2010. PLoS One 2016; 11(9):e0162744.
25. Saffari F, Widerström M, Gurram BK, Edebro H, Hojabri Z, Monsen T. Molecular and phenotypic characterization of multidrug-resistant clones of Staphylococcus epidermidis in Iranian Hospitals: Clonal relatedness to healthcare-associated methicillin-resistant isolates in Northern Europe. Microb Drug Resist 2016; 22: 570-577.
26. Li M, Wang X, Gao Q, Lu Y. Molecular characterization of Staphylococcus epidermidis strains isolated from a teaching hospital in Shanghai, China. J Med Microbiol 2009; 58: 456-461.
27. Wong A, Reddy SP, Smyth DS, Aguero-Rosenfeld ME, Sakoulas G, Robinson DA. Polyphyletic emergence of linezolid-resistant staphylococci in the United States. Antimicrob Agents Chemother 2010; 54: 742-748.
28. Bouiller K, Ilic D, Wicky PH, Cholley P, Chirouze C, Bertrand X. Spread of clonal linezolid-resistant Staphylococcus epidermidis in an intensive care unit associated with linezolid exposure. Eur J Clin Microbiol Infect Dis 2020; 39: 1271-1277.
29. Ahlstrand E, Hellmark B, Svensson K, Söderquist B. Long-term molecular epidemiology of Staphylococcus epidermidis blood culture isolates from patients with hematological malignancies. PLoS One 2014;9(6):e99045.
30. Udo EE, Dashti AA. Detection of genes encoding aminoglycoside-modifying enzymes in staphylococci by polymerase chain reaction and dot blot hybridization. Int J Antimicrob Agents 2000; 13: 273-279.
31. Ida T, Okamoto R, Shimauchi C, Okubo T, Kuga A, Inoue M. Identification of aminoglycoside-modifying enzymes by susceptibility testing: epidemiology of methicillin-resistant Staphylococcus aureus in Japan. J Clin Microbiol 2001; 39: 3115-3121.
32. Choi SM, Kim SH, Kim HJ, Lee DG, Choi JH, Yoo JH, et al. Multiplex PCR for the detection of genes encoding aminoglycoside modifying enzymes and methicillin resistance among Staphylococcus species. J Korean Med Sci 2003; 18: 631-636.
33. Klingenberg C, Sundsfjord A, Rønnestad A, Mikalsen J, Gaustad P, Flaegstad T. Phenotypic and genotypic aminoglycoside resistance in blood culture isolates of coagulase-negative staphylococci from a single neonatal intensive care unit, 1989-2000. J Antimicrob Chemother 2004; 54: 889-896.
34. Ardic N, Sareyyupoglu B, Ozyurt M, Haznedaroglu T, Ilga U. Investigation of aminoglycoside modifying enzyme genes in methicillin-resistant staphylococci. Microbiol Res 2006; 161: 49-54.
35. Prestinaci F, Pezzotti P, Pantosti A. Antimicrobial resistance: a global multifaceted phenomenon. Pathog Glob Health 2015; 109: 309-318.
36. von Wintersdorff CJ, Penders J, van Niekerk JM, Mills ND, Majumder S, van Alphen LB, et al. Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer. Front Microbiol 2016; 7:173.
37. Beigverdi R, Sattari-Maraji A, Jabalameli F, Emaneini M. Prevalence of genes encoding aminoglycoside-modifying enzymes in clinical isolates of Gram-positive cocci in Iran: A systematic review and meta-analysis. Microb Drug Resist 2020; 26: 126-135.
38. Tokajian ST, Khalil PA, Jabbour D, Rizk M, Farah MJ, Hashwa FA, et al. Molecular characterization of Staphylococcus aureus in Lebanon. Epidemiol Infect 2010; 138: 707-712.
39. Mendes RE, Deshpande LM, Costello AJ, Farrell DJ. Molecular epidemiology of Staphylococcus epidermidis clinical isolates from U.S. hospitals. Antimicrob Agents Chemother 2012; 56: 4656-4661.
40. Wang PJ, Xie CB, Sun FH, Guo LJ, Dai M, Cheng X, et al. Molecular characteristics of methicillin-resistant Staphylococcus epidermidis on the abdominal skin of females before laparotomy. Int J Mol Sci 2016;17:992.
41. Di Ruscio F, Bjørnholt JV, Leegaard TM, Moen AEF, de Blasio BF. MRSA infections in Norway: A study of the temporal evolution, 2006-2015. PLoS One 2017; 12(6):e0179771.
42. Dai Y, Liu J, Guo W, Meng H, Huang Q, He L, et al. Decreasing methicillin-resistant Staphylococcus aureus (MRSA) infections is attributable to the disappearance of predominant MRSA ST239 clones, Shanghai, 2008-2017. Emerg Microbes Infect 2019; 8: 471-478.
2. Liakopoulos A, Foka A, Vourli S, Zerva L, Tsiapara F, Protonotariou E, et al. Aminoglycoside-resistant staphylococci in Greece: prevalence and resistance mechanisms. Eur J Clin Microbiol Infect Dis 2011; 30: 701-705.
3. Ramirez MS, Nikolaidis N, Tolmasky ME. Rise and dissemination of aminoglycoside resistance: the 33paradigm. Front Microbiol 2013; 4: 121.
4. Garneau-Tsodikova S, Labby KJ. Mechanisms of resistance to aminoglycoside antibiotics: overview and perspectives. Medchemcomm 2016; 7: 11-27.
5. Sabat AJ, Budimir A, Nashev D, Sá-Leão R, van Dijl J, Laurent F, et al. Overview of molecular typing methods for outbreak detection and epidemiological surveillance. Euro Surveill 2013; 18: 20380.
6. Enright MC, Day NP, Davies CE, Peacock SJ, Spratt BG. Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus. J Clin Microbiol 2000; 38: 1008-1015.
7. Thomas JC, Robinson DA. Multilocus sequence typing of Staphylococcus epidermidis. Methods Mol Biol 2014; 1106:61-69.
8. Conceição T, Aires-de-Sousa M, Füzi M, Tóth A, Pászti J, Ungvári E, et al. Replacement of methicillin-resistant Staphylococcus aureus clones in Hungary over time: a 10-year surveillance study. Clin Microbiol Infect 2007; 13: 971-979.
9. Mahon CR, Lehman DC, Manuselis Jr G. Textbook of Diagnostic Microbiology. 6th edition.New York: Saunders; 2019. p: 307-319.
10. Hirotaki S, Sasaki T, Kuwahara-Arai K, Hiramatsu K. Rapid and accurate identification of human-associated staphylococci by use of multiplex PCR. J Clin Microbiol 2011; 49: 3627-3631.
11. Clinical and Laboratory Standards Institute (CLSI). Performance standards for antimicrobial susceptibility testing. 27th ed. CLSI supplement M100. Wayne, PA: Clinical and Laboratory Standards Institute; 2017.
12. Emaneini M, Taherikalani M, Eslampour MA, Sedaghat H, Aligholi M, Jabalameli F, et al. Phenotypic and genotypic evaluation of aminoglycoside resistance in clinical isolates of staphylococci in Tehran, Iran. Microb Drug Resist 2009; 15: 129-132.
13. Nascimento M, Sousa A, Ramirez M, Francisco AP, Carriço JA, Vaz C. PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods. Bioinformatics 2017; 33: 128-129.
14. Cheng H, Yuan W, Zeng F, Hu Q, Shang W, Tang D, et al. Molecular and phenotypic evidence for the spread of three major methicillin-resistant Staphylococcus aureus clones associated with two characteristic antimicrobial resistance profiles in China. J Antimicrob Chemother 2013;68:2453-2457.
15. Seyedi-Marghaki F, Kalantar-Neyestanaki D, Saffari F, Hosseini-Nave H, Moradi M. Distribution of aminoglycoside-modifying enzymes and molecular analysis of the coagulase gene in clinical isolates of methicillin-resistant and methicillin-susceptible Staphylococcus aureus. Microb Drug Resist 2019; 25: 47-53.
16. Yadegar A, Sattari M, Mozafari NA, Goudarzi GR. Prevalence of the genes encoding aminoglycoside-modifying enzymes and methicillin resistance among clinical isolates of Staphylococcus aureus in Tehran, Iran. Microb Drug Resist 2009; 15: 109-113.
17. Yuan W, Liu J, Zhan Y, Wang L, Jiang Y, Zhang Y, et al. Molecular typing revealed the emergence of pvl-positive sequence type 22 methicillin-susceptible Staphylococcus aureus in Urumqi, Northwestern China. Infect Drug Resist 2019;12:1719-1728.
18. Chen CJ, Huang YC. New epidemiology of Staphylococcus aureus infection in Asia. Clin Microbiol Infect 2014;20:605-623.
19. Lakhundi S, Zhang K. Methicillin-resistant Staphylococcus aureus: molecular characterization, evolution, and epidemiology. Clin Microbiol Rev 2018; 31(4):e00020-18.
20. Havaei SA, Vidovic S, Tahmineh N, Mohammad K, Mohsen K, Starnino S, et al. Epidemic methicillin-susceptible Staphylococcus aureus lineages are the main cause of infections at an Iranian university hospital. J Clin Microbiol 2011; 49: 3990-3993.
21. Goudarzi M, Bahramian M, Satarzadeh Tabrizi M, Udo EE, Figueiredo AM, Fazeli M, et al. Genetic diversity of methicillin resistant Staphylococcus aureus strains isolated from burn patients in Iran: ST239-SCCmec III/t037 emerges as the major clone. Microb Pathog 2017; 105: 1-7.
22. Goudarzi M, Goudarzi H, AM SF, Udo EE, Fazeli M, Asadzadeh M, et al. Molecular characterization of methicillin resistant Staphylococcus aureus strains isolated from intensive care units in Iran: ST22-SCCmec IV/t790 emerges as the major clone. PLoS One 2016; 11(5):e0155529.
23. Zhou YP, Wilder-Smith A, Hsu LY. The role of international travel in the spread of methicillin-resistant Staphylococcus aureus. J Travel Med 2014; 21: 272-281.
24. Boswihi SS, Udo EE, Al-Sweih N. Shifts in the clonal distribution of methicillin-resistant Staphylococcus aureus in Kuwait hospitals: 1992-2010. PLoS One 2016; 11(9):e0162744.
25. Saffari F, Widerström M, Gurram BK, Edebro H, Hojabri Z, Monsen T. Molecular and phenotypic characterization of multidrug-resistant clones of Staphylococcus epidermidis in Iranian Hospitals: Clonal relatedness to healthcare-associated methicillin-resistant isolates in Northern Europe. Microb Drug Resist 2016; 22: 570-577.
26. Li M, Wang X, Gao Q, Lu Y. Molecular characterization of Staphylococcus epidermidis strains isolated from a teaching hospital in Shanghai, China. J Med Microbiol 2009; 58: 456-461.
27. Wong A, Reddy SP, Smyth DS, Aguero-Rosenfeld ME, Sakoulas G, Robinson DA. Polyphyletic emergence of linezolid-resistant staphylococci in the United States. Antimicrob Agents Chemother 2010; 54: 742-748.
28. Bouiller K, Ilic D, Wicky PH, Cholley P, Chirouze C, Bertrand X. Spread of clonal linezolid-resistant Staphylococcus epidermidis in an intensive care unit associated with linezolid exposure. Eur J Clin Microbiol Infect Dis 2020; 39: 1271-1277.
29. Ahlstrand E, Hellmark B, Svensson K, Söderquist B. Long-term molecular epidemiology of Staphylococcus epidermidis blood culture isolates from patients with hematological malignancies. PLoS One 2014;9(6):e99045.
30. Udo EE, Dashti AA. Detection of genes encoding aminoglycoside-modifying enzymes in staphylococci by polymerase chain reaction and dot blot hybridization. Int J Antimicrob Agents 2000; 13: 273-279.
31. Ida T, Okamoto R, Shimauchi C, Okubo T, Kuga A, Inoue M. Identification of aminoglycoside-modifying enzymes by susceptibility testing: epidemiology of methicillin-resistant Staphylococcus aureus in Japan. J Clin Microbiol 2001; 39: 3115-3121.
32. Choi SM, Kim SH, Kim HJ, Lee DG, Choi JH, Yoo JH, et al. Multiplex PCR for the detection of genes encoding aminoglycoside modifying enzymes and methicillin resistance among Staphylococcus species. J Korean Med Sci 2003; 18: 631-636.
33. Klingenberg C, Sundsfjord A, Rønnestad A, Mikalsen J, Gaustad P, Flaegstad T. Phenotypic and genotypic aminoglycoside resistance in blood culture isolates of coagulase-negative staphylococci from a single neonatal intensive care unit, 1989-2000. J Antimicrob Chemother 2004; 54: 889-896.
34. Ardic N, Sareyyupoglu B, Ozyurt M, Haznedaroglu T, Ilga U. Investigation of aminoglycoside modifying enzyme genes in methicillin-resistant staphylococci. Microbiol Res 2006; 161: 49-54.
35. Prestinaci F, Pezzotti P, Pantosti A. Antimicrobial resistance: a global multifaceted phenomenon. Pathog Glob Health 2015; 109: 309-318.
36. von Wintersdorff CJ, Penders J, van Niekerk JM, Mills ND, Majumder S, van Alphen LB, et al. Dissemination of antimicrobial resistance in microbial ecosystems through horizontal gene transfer. Front Microbiol 2016; 7:173.
37. Beigverdi R, Sattari-Maraji A, Jabalameli F, Emaneini M. Prevalence of genes encoding aminoglycoside-modifying enzymes in clinical isolates of Gram-positive cocci in Iran: A systematic review and meta-analysis. Microb Drug Resist 2020; 26: 126-135.
38. Tokajian ST, Khalil PA, Jabbour D, Rizk M, Farah MJ, Hashwa FA, et al. Molecular characterization of Staphylococcus aureus in Lebanon. Epidemiol Infect 2010; 138: 707-712.
39. Mendes RE, Deshpande LM, Costello AJ, Farrell DJ. Molecular epidemiology of Staphylococcus epidermidis clinical isolates from U.S. hospitals. Antimicrob Agents Chemother 2012; 56: 4656-4661.
40. Wang PJ, Xie CB, Sun FH, Guo LJ, Dai M, Cheng X, et al. Molecular characteristics of methicillin-resistant Staphylococcus epidermidis on the abdominal skin of females before laparotomy. Int J Mol Sci 2016;17:992.
41. Di Ruscio F, Bjørnholt JV, Leegaard TM, Moen AEF, de Blasio BF. MRSA infections in Norway: A study of the temporal evolution, 2006-2015. PLoS One 2017; 12(6):e0179771.
42. Dai Y, Liu J, Guo W, Meng H, Huang Q, He L, et al. Decreasing methicillin-resistant Staphylococcus aureus (MRSA) infections is attributable to the disappearance of predominant MRSA ST239 clones, Shanghai, 2008-2017. Emerg Microbes Infect 2019; 8: 471-478.
| Files | ||
| Issue | Vol 14 No 3 (2022) | |
| Section | Original Article(s) | |
| DOI | https://doi.org/10.18502/ijm.v14i3.9760 | |
| Keywords | ||
| Aminoglycosides; Aminoglycoside modifying enzymes; Staphylococcus aureus; Staphylococcus epidermidis; Multilocus sequence typing | ||
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How to Cite
1.
Bourbour S, Beigverdi R, Beheshti M, Jabalameli F, Emaneini M. Identification of major sequence types among aminoglycoside resistant Staphylococcus aureus and Staphylococcus epidermidis strains isolated from clinical samples. Iran J Microbiol. 2022;14(3):305-312.
